Evolution and functional cross-talk of protein post-translational modifications

A Genomic Survey of HECT Ubiquitin Ligases in Eukaryotes Reveals Independent Expansions of the HECT System in Several Lineages

(2013) Xavier Grau-Bové et al.   Genome Biology and Evolution

Comprehensive Profiling of Protein Lysine Acetylation in Escherichia coli

(2013) Kai Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Reversible acetylation regulates acetate and propionate metabolism in Mycobacterium smegmatis

(2013) J. D. Hayden et al.   MICROBIOLOGY-SGM

Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

(2013) Brian T. Weinert et al.   MOLECULAR CELL

SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine

(2013) Hong Jiang et al.   NATURE

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation

(2013) Danielle L Swaney et al.   NATURE METHODS

Proteomic analysis of acetylation in thermophilicGeobacillus kaustophilus

(2013) Dong-Woo Lee et al.   PROTEOMICS

The acetylproteome of Gram-positive model bacteriumBacillus subtilis

(2013) Dooil Kim et al.   PROTEOMICS

Dual Coordination of Post Translational Modifications in Human Protein Networks

(2013) Jonathan Woodsmith et al.   PLoS Computational Biology

Functional Interplay between Caspase Cleavage and Phosphorylation Sculpts the Apoptotic Proteome

(2012) Melissa M. Dix et al.   CELL

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

Phosphorylation meets nuclear import: a review

(2012) Jonathan D Nardozzi et al.   Cell Communication and Signaling

Differential lysine acetylation profiles of Erwinia amylovora strains revealed by proteomics

(2012) Xia Wu et al.   Journal of Proteomics

Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope inSaccharomyces cerevisiae

(2012) Peter Henriksen et al.   MOLECULAR & CELLULAR PROTEOMICS

The origins and evolution of ubiquitination sites

(2012) Tzachi Hagai et al.   Molecular BioSystems

Proteomic Investigations Reveal a Role for RNA Processing Factor THRAP3 in the DNA Damage Response

(2012) Petra Beli et al.   MOLECULAR CELL

Mapping N-Glycosylation Sites across Seven Evolutionarily Distant Species Reveals a Divergent Substrate Proteome Despite a Common Core Machinery

(2012) Dorota F. Zielinska et al.   MOLECULAR CELL

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Deciphering a global network of functionally associated post-translational modifications

(2012) Pablo Minguez et al.   Molecular Systems Biology

Regulation of yeast central metabolism by enzyme phosphorylation

(2012) Ana Paula Oliveira et al.   Molecular Systems Biology

Phosphorylation sites of higher stoichiometry are more conserved

(2012) Chris Soon Heng Tan et al.   NATURE METHODS

Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information

(2012) E. D. Levy et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine Kinases

(2012) H. Suga et al.   Science Signaling

Network Evolution: Rewiring and Signatures of Conservation in Signaling

(2012) Mark G. F. Sun et al.   PLoS Computational Biology

Characterization and Prediction of Protein Phosphorylation Hotspots in Arabidopsis thaliana

(2012) Jan-Ole Christian et al.   Frontiers in Plant Science

Catalytic and glycan-binding abilities of ppGalNAc-T2 are regulated by acetylation

(2011) Natacha Zlocowski et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A Mechanism for the Evolution of Phosphorylation Sites

(2011) Samuel M. Pearlman et al.   CELL

Global Identification of Modular Cullin-RING Ligase Substrates

(2011) Michael J. Emanuele et al.   CELL

The natural history of ubiquitin and ubiquitin-related domains

(2011) Alexander Maxwell Burroughs   Frontiers in Bioscience-Landmark

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

(2011) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Rampant Purifying Selection Conserves Positions with Posttranslational Modifications in Human Proteins

(2011) V. E. Gray et al.   MOLECULAR BIOLOGY AND EVOLUTION

Acetyl-CoA Induces Cell Growth and Proliferation by Promoting the Acetylation of Histones at Growth Genes

(2011) Ling Cai et al.   MOLECULAR CELL

Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome

(2011) Woong Kim et al.   MOLECULAR CELL

Cascades of multisite phosphorylation control Sic1 destruction at the onset of S phase

(2011) Mardo Kõivomägi et al.   NATURE

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

Extensive DNA-binding specificity divergence of a conserved transcription regulator

(2011) C. R. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sirt5 Is a NAD-Dependent Protein Lysine Demalonylase and Desuccinylase

(2011) J. Du et al.   SCIENCE

Spatial Exclusivity Combined with Positive and Negative Selection of Phosphorylation Motifs Is the Basis for Context-Dependent Mitotic Signaling

(2011) J. Alexander et al.   Science Signaling

System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation

(2011) K. T. G. Rigbolt et al.   Science Signaling

Phosphorylation in Protein-Protein Binding: Effect on Stability and Function

(2011) Hafumi Nishi et al.   STRUCTURE

Measuring the Evolutionary Rewiring of Biological Networks

(2011) Chong Shou et al.   PLoS Computational Biology

Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data

(2010) Regev Schweiger et al.   Biology Direct

MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains

(2010) Hugo YK Lam et al.   BMC BIOINFORMATICS

Phosphotyrosine Signaling: Evolving a New Cellular Communication System

(2010) Wendell A. Lim et al.   CELL

Prolyl hydroxylation- and glycosylation-dependent functions of Skp1 in O2-regulated development of Dictyostelium

(2010) Zhuo A. Wang et al.   DEVELOPMENTAL BIOLOGY

Site-specific Phosphorylation Dynamics of the Nuclear Proteome during the DNA Damage Response

(2010) Martin V. Bennetzen et al.   MOLECULAR & CELLULAR PROTEOMICS

Evolution of Characterized Phosphorylation Sites in Budding Yeast

(2010) A. N. Nguyen Ba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites

(2010) A. Zanzoni et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants

(2010) H. Nakagami et al.   PLANT PHYSIOLOGY

Prokayrotic Ubiquitin-Like Protein (Pup) Proteome of Mycobacterium tuberculosis

(2010) Richard A. Festa et al.   PLoS One

Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux

(2010) Q. Wang et al.   SCIENCE

Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs

(2010) J. Mok et al.   Science Signaling

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage

(2010) A. Bensimon et al.   Science Signaling

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

Moving from transcriptional to phospho-evolution: generalizing regulatory evolution?

(2010) Alan M. Moses et al.   TRENDS IN GENETICS

The origin and early evolution of eukaryotes in the light of phylogenomics

(2010) Eugene V Koonin   GENOME BIOLOGY

Histone methylation and ubiquitination with their cross-talk and roles in gene expression and stability

(2009) A. Shukla et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Factors Affecting the Diversity of DNA Replication Licensing Control in Eukaryotes

(2009) Lucy S. Drury et al.   CURRENT BIOLOGY

Structure and in Vivo Requirement of the Yeast Spt6 SH2 Domain

(2009) Stefan Dengl et al.   JOURNAL OF MOLECULAR BIOLOGY

Nonproteolytic Functions of Ubiquitin in Cell Signaling

(2009) Zhijian J. Chen et al.   MOLECULAR CELL

Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays

(2009) Avinash Persaud et al.   Molecular Systems Biology

Origin and function of ubiquitin-like proteins

(2009) Mark Hochstrasser   NATURE

Positive Selection of Tyrosine Loss in Metazoan Evolution

(2009) C. S. H. Tan et al.   SCIENCE

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

(2009) C. Choudhary et al.   SCIENCE

Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases

(2009) C. S. H. Tan et al.   Science Signaling

Cell regulation: determined to signal discrete cooperation

(2009) Toby J. Gibson   TRENDS IN BIOCHEMICAL SCIENCES

A post-translational modification code for transcription factors: sorting through a sea of signals

(2009) Bérénice A. Benayoun et al.   TRENDS IN CELL BIOLOGY

Weak functional constraints on phosphoproteomes

(2009) Christian R. Landry et al.   TRENDS IN GENETICS

Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species

(2009) Pedro Beltrao et al.   PLOS BIOLOGY

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

(2009) Raffi Tonikian et al.   PLOS BIOLOGY

Evolution of protein phosphatases in plants and animals

(2008) Greg B. G. Moorhead et al.   BIOCHEMICAL JOURNAL

Not just for Eukarya anymore: protein glycosylation in Bacteria and Archaea

(2008) Mehtap Abu-Qarn et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Anatomy of the E2 ligase fold: Implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation

(2008) A. Maxwell Burroughs et al.   JOURNAL OF STRUCTURAL BIOLOGY

Lysine Acetylation Is a Highly Abundant and Evolutionarily Conserved Modification inEscherichia Coli

(2008) Junmei Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Acetylation of Conserved Lysines in the Catalytic Core of Cyclin-Dependent Kinase 9 Inhibits Kinase Activity and Regulates Transcription

(2008) A. Sabo et al.   MOLECULAR AND CELLULAR BIOLOGY

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

(2008) D. Pincus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural history of the E1-like superfamily: Implication for adenylation, sulfur transfer, and ubiquitin conjugation

(2008) A. Maxwell Burroughs et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evolution of Eukaryotic Transcription Circuits

(2008) B. B. Tuch et al.   SCIENCE

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY

Protein Complex Evolution Does Not Involve Extensive Network Rewiring

(2008) Teunis J. P. van Dam et al.   PLoS Computational Biology

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

(2007) Lakshminarayan M. Iyer et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY